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List of works by Tak-Wah Lam

A 5-competitive on-line scheduler for merging video streams

A Decomposition Theorem for MaximumWeight Bipartite Matchings with Applications to Evolutionary Trees

A Space and Time Efficient Algorithm for Constructing Compressed Suffix Arrays

A Tighter Extra-Resource Analysis of Online Deadline Scheduling

A linear size index for approximate pattern matching

A simple and economical method for improving whole genome alignment

scientific article

A simple and economical method for improving whole-genome alignment

AC-DIAMOND: Accelerating Protein Alignment via Better SIMD Parallelization and Space-Efficient Indexing

APPROXIMATING THE NEAREST NEIGHBOR INTERCHARGE DISTANCE FOR NON-UNIFORM-DEGREE EVOLUTIONARY TREES

Adjacent nucleotide dependence in ncRNA and order-1 SCFG for ncRNA identification.

scientific article

Aggressive Online Deadline Scheduling

Algorithms for pseudoknot classification

An Even Faster and More Unifying Algorithm for Comparing Trees via Unbalanced Bipartite Matchings

An efficient algorithm for optimizing whole genome alignment with noise.

scientific article

Approximating Frequent Items in Asynchronous Data Stream over a Sliding Window

Approximating Frequent Items in Asynchronous Data Stream over a Sliding Window

article published in 2010

Approximating the Nearest Neighbor Interchange Distance for Evolutionary Trees with Non-uniform Degrees

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

scientific article

Automatic construction of online catalog topologies

BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU.

scientific article

BASE: a practical de novo assembler for large genomes using long NGS reads

scientific article

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

scientific article

Cache-oblivious index for approximate string matching

Competitive non-migratory scheduling for flow time and energy

Compressed Index for Dictionary Matching

Compressed indexes for dynamic text collections

Compressed indexing and local alignment of DNA.

scientific article published on 28 January 2008

Compressing Dictionary Matching Index via Sparsification Technique

Construction of online catalog topologies using decision trees

Correcting short reads with high error rates for improved sequencing result.

scientific article published in January 2009

Detection of novel tandem duplication with next-generation sequencing

Dictionary Matching with Uneven Gaps

Dictionary Matching with a Bounded Gap in Pattern or in Text

EFFICIENT CONSTRAINED MULTIPLE SEQUENCE ALIGNMENT WITH PERFORMANCE GUARANTEE

scientific article published on 01 February 2005

Edit Distance to Monotonicity in Sliding Windows

Efficient SNP-sensitive alignment and database-assisted SNP calling for low coverage samples

article published in 2012

Energy-Efficient Due Date Scheduling

article by Ho-Leung Chan et al published 2011 in Lecture Notes in Computer Science

Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

scientific article published on 8 July 2015

Erratum: The sequence and de novo assembly of the giant panda genome

scientific article published in Nature

Extra Processors versus Future Information in Optimal Deadline Scheduling

Extra Unit-Speed Machines Are Almost as Powerful as Speedy Machines for Flow Time Scheduling

article by Ho-Leung Chan et al published January 2008 in SIAM Journal on Computing

Extra unit-speed machines are almost as powerful as speedy machines for competitive flow time scheduling

scholarly article published 2006

FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data

scientific article

Filtering of ineffective siRNAs and improved siRNA design tool.

scientific article published on 27 August 2004

Finding alternative splicing patterns with strong support from expressed sequences on individual exons/introns

scientific article published in October 2008

Finding least-weight subsequences with fewer processors

article by Kwong-fai Chan & Tak-Wah Lam published 1990 in Lecture Notes in Computer Science

From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

scientific article

GLProbs

GLProbs: Aligning Multiple Sequences Adaptively

scientific article published on January 2015

Guest Editors Foreword

Improved Approximate String Matching Using Compressed Suffix Data Structures

Improved multi-processor scheduling for flow time and energy

Improving multiple sequence alignment by using better guide trees

scientific article published on 18 March 2015

Improving the accuracy of signal transduction pathway construction using level-2 neighbours

scientific article published on January 1, 2010

LCR_Finder: A de Novo Low Copy Repeat Finder for Human Genome

Local structural alignment of RNA with affine gap model ⬇️

scientific article published on May 28, 2011

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

scientific article published on 21 March 2016

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

scientific article

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC).

scientific article published on 23 April 2015

MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs

scientific article published on 16 October 2017

Memory efficient algorithms for structural alignment of RNAs with pseudoknots

scientific article published on 30 March 2011

Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions

scientific article published on 5 August 2011

Non-clairvoyant Speed Scaling for Weighted Flow Time

Non-clairvoyant Weighted Flow Time Scheduling on Different Multi-processor Models

Non-clairvoyant Weighted Flow Time Scheduling on Different Multi-processor Models

Non-clairvoyant weighted flow time scheduling with rejection penalty

Non-shared edges and nearest neighbor interchanges revisited

Nonmigratory Multiprocessor Scheduling for Response Time and Energy

article

Nonmigratory Online Deadline Scheduling on Multiprocessors

On the speed requirement for optimal deadline scheduling in overloaded systems

On-line Stream Merging with Max Span and Min Coverage

On-line stream merging in a general setting

Online Flow Time Scheduling in the Presence of Preemption Overhead

Online Speed Scaling Based on Active Job Count to Minimize Flow Plus Energy

Online Tracking of the Dominance Relationship of Distributed Multi-dimensional Data

Optimizing throughput and energy in online deadline scheduling

Performance guarantee for edf under overload

PnpProbs: a better multiple sequence alignment tool by better handling of guide trees

scientific article

Predicting RNA secondary structures with arbitrary pseudoknots by maximizing the number of stacking pairs

scientific article published in January 2003

Predicting RNA secondary structures with arbitrary pseudoknots by maximizing the number of stacking pairs

RNASAlign: RNA structural alignment system.

scientific article published on 8 June 2011

Reconstructing an ultrametric galled phylogenetic network from a distance matrix

scientific article published in August 2006

SOAP2: an improved ultrafast tool for short read alignment

scientific article (publication date: August 2009)

SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner

scientific article (publication date: 2013)

SOAP3: ultra-fast GPU-based parallel alignment tool for short reads

scientific article

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

scientific article

SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads

scientific article

SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data

scientific article

SUBTREE TRANSFER DISTANCE FOR DEGREE-D PHYLOGENIES

scholarly article by Wing-Kai Hon et al published December 2004 in International Journal of Foundations of Computer Science

Scheduling for Speed Bounded Processors

Scheduling for weighted flow time and energy with rejection penalty

Scheduling with Gaps: New Models and Algorithms

scholarly article by Marek Chrobak et al published 2015 in Lecture Notes in Computer Science

Serine peptidase inhibitor Kazal type 1 (SPINK1) as novel downstream effector of the cadherin-17/β-catenin axis in hepatocellular carcinoma

Sleep Management on Multiple Machines for Energy and Flow Time

Sleep with Guilt and Work Faster to Minimize Flow Plus Energy

Structural alignment of RNA with complex pseudoknot structure

scientific article

Succinct Index for Dynamic Dictionary Matching

Succinct Text Indexing with Wildcards

The mutated subsequence problem and locating conserved genes

scientific article published on 3 March 2005

The sequence and de novo assembly of the giant panda genome

scientific article

Tradeoff between Energy and Throughput for Online Deadline Scheduling

Tradeoff between energy and throughput for online deadline scheduling

Transcriptome Analysis of Acute Phase Liver Graft Injury in Liver Transplantation.

scientific article published on 6 April 2018

database.bio: a web application for interpreting human variations

scientific article published on 26 August 2015

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